Formalising Concepts of Species, Sex and Developmental Stage in Anatomical Ontologies
Bioinformatics. doi:10.1093/bioinformatics/bti409
Supplementary Materials


The Anatomy Context Ontology has been extended with a developmental mouse anatomy (Kaufmann, Bard and Davidson, MRC HGU) and a human anatomy (Bard) to illustrate its use. These files are linked from the table below. The extended ontologies are provided in formats for DAG-Edit/OBO-Edit and for the COBrA ontology editor (version 1.16). Protege files are also provided.

COBrA 1.16 is specifically designed to display the Carnegie and Theiler Stages at which a tissue is present alongside the term names in the hierarchical view of the ontology. The startStage and endStage relations where this information is represented can be seen in COBrA's righthand panel (node-based view) of the ontology. COBrA can be installed by downloading the file cobra-1.16.tar following the link below. See also Aitken, S., Korf, R., Webber, B. and Bard, J. COBrA: A Bio-Ontology Editor. Bioinformatics. 2005 21(6):825-826. doi: 10.1093/bioinformatics/bti097 and www.xspan.org for further information about COBrA.

The definitive OWL version of the Anatomy Context Ontology described in the paper is provided in context-core.owl. OWL versions of the extended ontologies are also provided. The complete set of definitions is provided in first-order logic (in Otter syntax) in context.otter. The plain OWL files are provided to developers, and are not readily viewable in the most commonly-used tools e.g. DAG-Edit or COBrA.

COBrA Files Download COBrA 1.16
Anatomy Context Ontology context-core-cobra.owl
Anatomy Context Ontology plus Mouse Anatomy context-plus-mouse-cobra.owl
Anatomy Context Ontology plus Human Anatomy context-plus-human-cobra.owl

DAG Edit / OBO Edit Files
Anatomy Context Ontology context-core.dag
context-core.obo
Anatomy Context Ontology plus Mouse Anatomy context-plus-mouse.dag
context-plus-mouse.obo
Anatomy Context Ontology plus Human Anatomy context-plus-human.dag
context-plus-human.obo

Protege Files
Anatomy Context Ontology context-core-protege.pprj
context-core-protege.owl
Anatomy Context Ontology plus Mouse Anatomy context-plus-mouse-protege.pprj
context-plus-mouse-protege.owl
Anatomy Context Ontology plus Human Anatomy context-plus-human-protege.pprj
context-plus-human-protege.owl

OWL Files
Anatomy Context Ontology context-core.owl
Anatomy Context Ontology plus Mouse Anatomy context-plus-mouse.owl
Anatomy Context Ontology plus Human Anatomy context-plus-human.owl

Definitions in Anatomy Context Ontology in first-order logic (Otter syntax) context.otter




Stuart Aitken
Artificial Intelligence Applications Institute
University of Edinburgh

Email: s.aitken@ed.ac.uk